CATH Documentation

The alpha helix is the most abundant type of secondary structure in proteins and has been extensively documented.
In brief, alpha helices are formed from stretches of consecutive amino acid residues
with phi and psi angle pairs which correspond to the bottom left quadrant of the Ramachandran Plot.
The mean phi and psi angles for alpha helices found in proteins are -62 degrees and -41 degrees,
respectively. The alpha
helix has 3.6 residues per turn, with a hydrogen bond between the CO of residue
n and the NH of residue n +4. The closed loop formed by one of these
hydrogen bonds and the intervening stretch of backbone contains 13 atoms (including the hydrogen).
Hence the nomenclature for an alpha helix is 3.6(13)-helix, where the 3.6 is the
number of residues per turn and 13 is the number of atoms in the
hydrogen bonded loop.
Some alpha helices are curved or show distinct kinks, for example those caused by
the presence of proline residues. The example shown is a enterotoxin (CATH domain ID 1tiiC00).